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From: Sadaf Rani <sadafrani6.gmail.com>

Date: Sat, 11 May 2019 12:16:07 +0100

amber.ambermd.org

Subject: The unperturbed charge of the unit: 4.003000 is not zero

I am trying to generate parameters of my protein using following commands:-

antechamber -i lig.pdb -fi pdb -o 1HVR_ligand.mol2 -fo mol2 -c bcc -pf yes

-nc 0 -at gaff2 -j 5

parmchk2 -i 1HVR_ligand.mol2 -f mol2 -o 1HVR_ligand.frcmod -s 2

However I get following error message:-

Added 21001 residues.

*> addIonsRand complex Na+ 0
*

addIonsRand: 1st Ion & target are the same charge:

can't neutralize.

*> saveamberparm complex complex.prmtop complex.inpcrd
*

Checking Unit.

WARNING: The unperturbed charge of the unit: 4.003000 is not zero.

FATAL: Atom .R<LIG 199>.A<C79 46> does not have a type.

FATAL: Atom .R<LIG 199>.A<C78 45> does not have a type.

FATAL: Atom .R<LIG 199>.A<C77 44> does not have a type.

FATAL: Atom .R<LIG 199>.A<C76 43> does not have a type.

FATAL: Atom .R<LIG 199>.A<C75 42> does not have a type.

FATAL: Atom .R<LIG 199>.A<C74 41> does not have a type.

FATAL: Atom .R<LIG 199>.A<C73 40> does not have a type.

FATAL: Atom .R<LIG 199>.A<C72 39> does not have a type.

FATAL: Atom .R<LIG 199>.A<C71 38> does not have a type.

FATAL: Atom .R<LIG 199>.A<C70 37> does not have a type.

FATAL: Atom .R<LIG 199>.A<C67 36> does not have a type.

FATAL: Atom .R<LIG 199>.A<C66 35> does not have a type.

FATAL: Atom .R<LIG 199>.A<C65 34> does not have a type.

FATAL: Atom .R<LIG 199>.A<C64 33> does not have a type.

FATAL: Atom .R<LIG 199>.A<C63 32> does not have a type.

FATAL: Atom .R<LIG 199>.A<C62 31> does not have a type.

FATAL: Atom .R<LIG 199>.A<C61 30> does not have a type.

FATAL: Atom .R<LIG 199>.A<C37 29> does not have a type.

FATAL: Atom .R<LIG 199>.A<C36 28> does not have a type.

FATAL: Atom .R<LIG 199>.A<C35 27> does not have a type.

FATAL: Atom .R<LIG 199>.A<C34 26> does not have a type.

FATAL: Atom .R<LIG 199>.A<C33 25> does not have a type.

FATAL: Atom .R<LIG 199>.A<C32 24> does not have a type.

FATAL: Atom .R<LIG 199>.A<C31 23> does not have a type.

FATAL: Atom .R<LIG 199>.A<C29 22> does not have a type.

FATAL: Atom .R<LIG 199>.A<C28 21> does not have a type.

FATAL: Atom .R<LIG 199>.A<C27 20> does not have a type.

FATAL: Atom .R<LIG 199>.A<C26 19> does not have a type.

FATAL: Atom .R<LIG 199>.A<C25 18> does not have a type.

FATAL: Atom .R<LIG 199>.A<C24 17> does not have a type.

FATAL: Atom .R<LIG 199>.A<C23 16> does not have a type.

FATAL: Atom .R<LIG 199>.A<C22 15> does not have a type.

FATAL: Atom .R<LIG 199>.A<C21 14> does not have a type.

FATAL: Atom .R<LIG 199>.A<C20 13> does not have a type.

FATAL: Atom .R<LIG 199>.A<C7 12> does not have a type.

FATAL: Atom .R<LIG 199>.A<N7 11> does not have a type.

FATAL: Atom .R<LIG 199>.A<C6 10> does not have a type.

FATAL: Atom .R<LIG 199>.A<O5 9> does not have a type.

FATAL: Atom .R<LIG 199>.A<C5 8> does not have a type.

FATAL: Atom .R<LIG 199>.A<O4 7> does not have a type.

FATAL: Atom .R<LIG 199>.A<C4 6> does not have a type.

FATAL: Atom .R<LIG 199>.A<C3 5> does not have a type.

FATAL: Atom .R<LIG 199>.A<C2 4> does not have a type.

FATAL: Atom .R<LIG 199>.A<N2 3> does not have a type.

FATAL: Atom .R<LIG 199>.A<O1 2> does not have a type.

FATAL: Atom .R<LIG 199>.A<C1 1> does not have a type.

FATAL: Atom .R<HIE 168>.A<HD1 18> does not have a type.

FATAL: Atom .R<CSO 166>.A<HD 9> does not have a type.

FATAL: Atom .R<CSO 166>.A<H 8> does not have a type.

FATAL: Atom .R<CSO 166>.A<OD 7> does not have a type.

FATAL: Atom .R<CSO 166>.A<O 6> does not have a type.

FATAL: Atom .R<CSO 166>.A<C 5> does not have a type.

FATAL: Atom .R<CSO 166>.A<SG 4> does not have a type.

FATAL: Atom .R<CSO 166>.A<CB 3> does not have a type.

FATAL: Atom .R<CSO 166>.A<CA 2> does not have a type.

FATAL: Atom .R<CSO 166>.A<N 1> does not have a type.

FATAL: Atom .R<HIE 69>.A<HD1 18> does not have a type.

FATAL: Atom .R<CSO 67>.A<HD 9> does not have a type.

FATAL: Atom .R<CSO 67>.A<H 8> does not have a type.

FATAL: Atom .R<CSO 67>.A<OD 7> does not have a type.

FATAL: Atom .R<CSO 67>.A<O 6> does not have a type.

FATAL: Atom .R<CSO 67>.A<C 5> does not have a type.

FATAL: Atom .R<CSO 67>.A<SG 4> does not have a type.

FATAL: Atom .R<CSO 67>.A<CB 3> does not have a type.

FATAL: Atom .R<CSO 67>.A<CA 2> does not have a type.

FATAL: Atom .R<CSO 67>.A<N 1> does not have a type.

Failed to generate parameters

Parameter file was not saved.

Can any one please suggest me.

Thank you

Sadaf

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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat May 11 2019 - 04:30:02 PDT

Date: Sat, 11 May 2019 12:16:07 +0100

amber.ambermd.org

Subject: The unperturbed charge of the unit: 4.003000 is not zero

I am trying to generate parameters of my protein using following commands:-

antechamber -i lig.pdb -fi pdb -o 1HVR_ligand.mol2 -fo mol2 -c bcc -pf yes

-nc 0 -at gaff2 -j 5

parmchk2 -i 1HVR_ligand.mol2 -f mol2 -o 1HVR_ligand.frcmod -s 2

However I get following error message:-

Added 21001 residues.

addIonsRand: 1st Ion & target are the same charge:

can't neutralize.

Checking Unit.

WARNING: The unperturbed charge of the unit: 4.003000 is not zero.

FATAL: Atom .R<LIG 199>.A<C79 46> does not have a type.

FATAL: Atom .R<LIG 199>.A<C78 45> does not have a type.

FATAL: Atom .R<LIG 199>.A<C77 44> does not have a type.

FATAL: Atom .R<LIG 199>.A<C76 43> does not have a type.

FATAL: Atom .R<LIG 199>.A<C75 42> does not have a type.

FATAL: Atom .R<LIG 199>.A<C74 41> does not have a type.

FATAL: Atom .R<LIG 199>.A<C73 40> does not have a type.

FATAL: Atom .R<LIG 199>.A<C72 39> does not have a type.

FATAL: Atom .R<LIG 199>.A<C71 38> does not have a type.

FATAL: Atom .R<LIG 199>.A<C70 37> does not have a type.

FATAL: Atom .R<LIG 199>.A<C67 36> does not have a type.

FATAL: Atom .R<LIG 199>.A<C66 35> does not have a type.

FATAL: Atom .R<LIG 199>.A<C65 34> does not have a type.

FATAL: Atom .R<LIG 199>.A<C64 33> does not have a type.

FATAL: Atom .R<LIG 199>.A<C63 32> does not have a type.

FATAL: Atom .R<LIG 199>.A<C62 31> does not have a type.

FATAL: Atom .R<LIG 199>.A<C61 30> does not have a type.

FATAL: Atom .R<LIG 199>.A<C37 29> does not have a type.

FATAL: Atom .R<LIG 199>.A<C36 28> does not have a type.

FATAL: Atom .R<LIG 199>.A<C35 27> does not have a type.

FATAL: Atom .R<LIG 199>.A<C34 26> does not have a type.

FATAL: Atom .R<LIG 199>.A<C33 25> does not have a type.

FATAL: Atom .R<LIG 199>.A<C32 24> does not have a type.

FATAL: Atom .R<LIG 199>.A<C31 23> does not have a type.

FATAL: Atom .R<LIG 199>.A<C29 22> does not have a type.

FATAL: Atom .R<LIG 199>.A<C28 21> does not have a type.

FATAL: Atom .R<LIG 199>.A<C27 20> does not have a type.

FATAL: Atom .R<LIG 199>.A<C26 19> does not have a type.

FATAL: Atom .R<LIG 199>.A<C25 18> does not have a type.

FATAL: Atom .R<LIG 199>.A<C24 17> does not have a type.

FATAL: Atom .R<LIG 199>.A<C23 16> does not have a type.

FATAL: Atom .R<LIG 199>.A<C22 15> does not have a type.

FATAL: Atom .R<LIG 199>.A<C21 14> does not have a type.

FATAL: Atom .R<LIG 199>.A<C20 13> does not have a type.

FATAL: Atom .R<LIG 199>.A<C7 12> does not have a type.

FATAL: Atom .R<LIG 199>.A<N7 11> does not have a type.

FATAL: Atom .R<LIG 199>.A<C6 10> does not have a type.

FATAL: Atom .R<LIG 199>.A<O5 9> does not have a type.

FATAL: Atom .R<LIG 199>.A<C5 8> does not have a type.

FATAL: Atom .R<LIG 199>.A<O4 7> does not have a type.

FATAL: Atom .R<LIG 199>.A<C4 6> does not have a type.

FATAL: Atom .R<LIG 199>.A<C3 5> does not have a type.

FATAL: Atom .R<LIG 199>.A<C2 4> does not have a type.

FATAL: Atom .R<LIG 199>.A<N2 3> does not have a type.

FATAL: Atom .R<LIG 199>.A<O1 2> does not have a type.

FATAL: Atom .R<LIG 199>.A<C1 1> does not have a type.

FATAL: Atom .R<HIE 168>.A<HD1 18> does not have a type.

FATAL: Atom .R<CSO 166>.A<HD 9> does not have a type.

FATAL: Atom .R<CSO 166>.A<H 8> does not have a type.

FATAL: Atom .R<CSO 166>.A<OD 7> does not have a type.

FATAL: Atom .R<CSO 166>.A<O 6> does not have a type.

FATAL: Atom .R<CSO 166>.A<C 5> does not have a type.

FATAL: Atom .R<CSO 166>.A<SG 4> does not have a type.

FATAL: Atom .R<CSO 166>.A<CB 3> does not have a type.

FATAL: Atom .R<CSO 166>.A<CA 2> does not have a type.

FATAL: Atom .R<CSO 166>.A<N 1> does not have a type.

FATAL: Atom .R<HIE 69>.A<HD1 18> does not have a type.

FATAL: Atom .R<CSO 67>.A<HD 9> does not have a type.

FATAL: Atom .R<CSO 67>.A<H 8> does not have a type.

FATAL: Atom .R<CSO 67>.A<OD 7> does not have a type.

FATAL: Atom .R<CSO 67>.A<O 6> does not have a type.

FATAL: Atom .R<CSO 67>.A<C 5> does not have a type.

FATAL: Atom .R<CSO 67>.A<SG 4> does not have a type.

FATAL: Atom .R<CSO 67>.A<CB 3> does not have a type.

FATAL: Atom .R<CSO 67>.A<CA 2> does not have a type.

FATAL: Atom .R<CSO 67>.A<N 1> does not have a type.

Failed to generate parameters

Parameter file was not saved.

Can any one please suggest me.

Thank you

Sadaf

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat May 11 2019 - 04:30:02 PDT

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